As somebody who does academic research for a living, I tend to be suspicious of stuff that looks like it might involve a conflict of interest, and that's my first reaction here too. But I also think this is a pretty poor story, because it leaves some very important questions unanswered, and instead stays at the level of circumstantial evidence. Which is itself a good argument against industry-funded research: its credibility will be undermined by even the appearance of impropriety.
For one thing, at certain points in the story, it sounds as if the study was planned, and the protocols designed, prior to the establishment of the mechanism for industry support. If that's true, it makes a big difference: I'd have fewer qualms about a two-layer system (NIH commissions a study first, then goes out and solicits industry $ to support it) from the sort of thing that the story mentions in other cases (industry association wants a study, goes and hires a scientist to conduct it).
For another thing, the story never actually says what people fear will go wrong with this study
that is specifically associated with its funding source; they talk about the problematic lack of attention to gender differences in ethanol metabolism, for example, but they say this is consistent problem in
NIH studies. (For my money, the more insidious problem is not whether the results of any particular study will be corrupted, but the fact that
stuff will only get studied -- even if it's studied well and responsibly -- if funding can be attracted for it.)
They also don't get into the political background here. Why is the NIH -- a respectable government agency -- funding a study by setting up what seems like a fancy Kickstarter account for industry contributions? Maybe because the NIH has been hit very hard by reductions in the real value of government appropriations, as well as by the sequester, over the last 15 years. Same basic reason that "public" research universities now have to get the majority of their funding from private sources (and have ramped up tuition).
So, on the day that we USicans are all supposed to make cherry pie in honor of the tree cut down by the founding father who led the rebellion against unjust taxation (I think I'm remembering this right!), I'll just say: You want good science? Be prepared to pay for it.